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Updated documentation. Improved import completion.

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This commit is contained in:
Landon Wark
2023-03-22 09:36:37 -05:00
parent 9c9c373830
commit cb05ad76e1
13 changed files with 164 additions and 90 deletions
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5
src/submissions/CHANGELOG.md
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@@ -1,3 +1,8 @@
**202303.04**
- Completed partial imports that will add in missing reagents found in the kit indicated by the user.
- Added web documentation to the help menu.
**202303.03**
- Increased robustness by utilizing PyQT6 widget names to pull data from forms instead of previously used label/input zip.

43
src/submissions/README.md
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@@ -1 +1,42 @@
**This is the readme file**
## Logging in New Run:
*should fit 90% of usage cases*
1. Ensure a properly formatted Submission Excel form has been filled out. (It will save you a few headaches)
a. All fields should be filled in to ensure proper lookups of reagents.
2. Open the app using the shortcut in the Submissions folder. For example: "L:\Robotics Laboratory Support\Submissions\submissions_v122b.exe - Shortcut.lnk" (Version may have changed).
a. Ignore the large black window of fast scrolling text, it is there for debugging purposes.
b. The 'Submissions' tab should be open by default.
3. Click on 'File' in the menu bar, followed by 'Import' and use the locate the form you definitely made sure was properly filled out in step 1.
4. Click "Ok".
5. Most of the fields in the form should be automatically filled in from the form area to the left of the screen.
6. You may need to maximize the app to ensure you can see all the info.
7. Any fields that are not automatically filled in can be filled in manually from the drop down menus.
8. Once you are certain all the information is correct, click 'Submit' at the bottom of the form.
9. Add in any reagents the app doesn't recognize.
10. Once the new run shows up at the bottom of the Submissions, everything is fine.
11. In case of any mistakes, the run can be overwritten by a reimport.
## Check existing Run:
1. Details of existing runs can be checked by double clicking on the row of interest in the summary sheet on the right of the 'Submissions' tab.
2. All information available on the run should be available in the resulting text window. This information can be exported by clicking 'Export PDF' at the top.
## Generating a report:
1. Click on 'Reports' -> 'Make Report' in the menu bar.
2. Select the start date and the end date you want for the report. Click 'ok'.
3. Use the file dialog to select a location to save the report.
a. Both an excel sheet and a pdf should be generated containing summary information for submissions made by each client lab.
## Checking Controls:
1. Controls for bacterial runs are now incorporated directly into the submissions database using webview. (Admittedly this performance is not as good as with a browser, so you will have to triage your data)
2. Click on the "Controls" tab.
3. Range of dates for controls can be selected from the date pickers at the top.
a. If start date is set after end date, the start date will default back to 3 months before end date.
b. Recommendation is to use less than 6 month date range keeping in mind that higher data density will affect performance (with kraken being the worst so far)
4. Analysis type and subtype can be set using the drop down menus. (Only kraken has a subtype so far).
## Adding new Kit:
1. Instructions to come.

2
src/submissions/__main__.py
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@@ -1,7 +1,7 @@
import sys
from pathlib import Path
import os
# must be set to enable qtwebengine in network path
# environment variable must be set to enable qtwebengine in network path
if getattr(sys, 'frozen', False):
os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = "1"
else :

10
src/submissions/backend/db/functions.py
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@@ -641,6 +641,16 @@ def lookup_submission_by_rsl_num(ctx:dict, rsl_num:str) -> models.BasicSubmissio
def lookup_submissions_using_reagent(ctx:dict, reagent:models.Reagent) -> list[models.BasicSubmission]:
"""
Retrieves each submission using a specified reagent.
Args:
ctx (dict): settings passed down from gui
reagent (models.Reagent): reagent object in question
Returns:
list[models.BasicSubmission]: list of all submissions using specified reagent.
"""
return ctx['database_session'].query(models.BasicSubmission).join(reagents_submissions).filter(reagents_submissions.c.reagent_id==reagent.id).all()

2
src/submissions/backend/db/models/submissions.py
View File

@@ -35,7 +35,7 @@ class BasicSubmission(Base):
reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions) #: relationship to reagents
reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id")) #: id of used reagents
extraction_info = Column(JSON) #: unstructured output from the extraction table logger.
run_cost = Column(FLOAT(2)) #: total cost of running the plate. Set from kit costs at time of creation.
run_cost = Column(FLOAT(2)) #: total cost of running the plate. Set from constant and mutable kit costs at time of creation.
uploaded_by = Column(String(32)) #: user name of person who submitted the submission to the database.
# Allows for subclassing into ex. BacterialCulture, Wastewater, etc.

31
src/submissions/backend/excel/parser.py
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@@ -27,6 +27,7 @@ class SheetParser(object):
# set attributes based on kwargs from gui ctx
for kwarg in kwargs:
setattr(self, f"_{kwarg}", kwargs[kwarg])
# self.__dict__.update(kwargs)
if filepath == None:
logger.error(f"No filepath given.")
self.xl = None
@@ -38,12 +39,12 @@ class SheetParser(object):
self.xl = None
self.sub = OrderedDict()
# make decision about type of sample we have
self.sub['submission_type'] = self._type_decider()
self.sub['submission_type'] = self.type_decider()
# select proper parser based on sample type
parse_sub = getattr(self, f"_parse_{self.sub['submission_type'].lower()}")
parse_sub = getattr(self, f"parse_{self.sub['submission_type'].lower()}")
parse_sub()
def _type_decider(self) -> str:
def type_decider(self) -> str:
"""
makes decisions about submission type based on structure of excel file
@@ -60,7 +61,7 @@ class SheetParser(object):
return "Unknown"
def _parse_unknown(self) -> None:
def parse_unknown(self) -> None:
"""
Dummy function to handle unknown excel structures
"""
@@ -68,7 +69,7 @@ class SheetParser(object):
self.sub = None
def _parse_generic(self, sheet_name:str) -> pd.DataFrame:
def parse_generic(self, sheet_name:str) -> pd.DataFrame:
"""
Pulls information common to all submission types and passes on dataframe
@@ -89,12 +90,12 @@ class SheetParser(object):
return submission_info
def _parse_bacterial_culture(self) -> None:
def parse_bacterial_culture(self) -> None:
"""
pulls info specific to bacterial culture sample type
"""
def _parse_reagents(df:pd.DataFrame) -> None:
def parse_reagents(df:pd.DataFrame) -> None:
"""
Pulls reagents from the bacterial sub-dataframe
@@ -126,7 +127,7 @@ class SheetParser(object):
else:
expiry = date.today()
self.sub[f"lot_{reagent_type}"] = {'lot':output_var, 'exp':expiry}
submission_info = self._parse_generic("Sample List")
submission_info = self.parse_generic("Sample List")
# iloc is [row][column] and the first row is set as header row so -2
tech = str(submission_info.iloc[11][1])
if tech == "nan":
@@ -139,7 +140,7 @@ class SheetParser(object):
# must be prefixed with 'lot_' to be recognized by gui
# Todo: find a more adaptable way to read reagents.
reagent_range = submission_info.iloc[1:13, 4:8]
_parse_reagents(reagent_range)
parse_reagents(reagent_range)
# get individual sample info
sample_parser = SampleParser(submission_info.iloc[15:111])
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
@@ -147,12 +148,12 @@ class SheetParser(object):
self.sub['samples'] = sample_parse()
def _parse_wastewater(self) -> None:
def parse_wastewater(self) -> None:
"""
pulls info specific to wastewater sample type
"""
def _parse_reagents(df:pd.DataFrame) -> None:
def parse_reagents(df:pd.DataFrame) -> None:
"""
Pulls reagents from the bacterial sub-dataframe
@@ -180,7 +181,7 @@ class SheetParser(object):
expiry = date.today()
self.sub[f"lot_{output_key}"] = {'lot':output_var, 'exp':expiry}
# parse submission sheet
submission_info = self._parse_generic("WW Submissions (ENTER HERE)")
submission_info = self.parse_generic("WW Submissions (ENTER HERE)")
# parse enrichment sheet
enrichment_info = self.xl.parse("Enrichment Worksheet", dtype=object)
# set enrichment reagent range
@@ -195,9 +196,9 @@ class SheetParser(object):
pcr_reagent_range = qprc_info.iloc[0:5, 9:20]
# compile technician info
self.sub['technician'] = f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}"
_parse_reagents(enr_reagent_range)
_parse_reagents(ext_reagent_range)
_parse_reagents(pcr_reagent_range)
parse_reagents(enr_reagent_range)
parse_reagents(ext_reagent_range)
parse_reagents(pcr_reagent_range)
# parse samples
sample_parser = SampleParser(submission_info.iloc[16:40])
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")

4
src/submissions/backend/excel/reports.py
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@@ -8,11 +8,13 @@ from datetime import date, timedelta
import sys
from pathlib import Path
import re
from tools import check_if_app
logger = logging.getLogger(f"submissions.{__name__}")
# set path of templates depending on pyinstaller/raw python
if getattr(sys, 'frozen', False):
# if getattr(sys, 'frozen', False):
if check_if_app():
loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
else:
loader_path = Path(__file__).parents[2].joinpath('templates').absolute().__str__()

6
src/submissions/configure/__init__.py
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@@ -8,6 +8,7 @@ from logging import handlers
from pathlib import Path
from sqlalchemy.orm import Session
from sqlalchemy import create_engine
from tools import check_if_app
logger = logging.getLogger(f"submissions.{__name__}")
@@ -102,7 +103,8 @@ def get_config(settings_path: Path|str|None=None) -> dict:
settings_path = Path.home().joinpath(".submissions", "config.yml")
# finally look in the local config
else:
if getattr(sys, 'frozen', False):
# if getattr(sys, 'frozen', False):
if check_if_app():
settings_path = Path(sys._MEIPASS).joinpath("files", "config.yml")
else:
settings_path = package_dir.joinpath('config.yml')
@@ -173,7 +175,7 @@ def setup_logger(verbosity:int=3):
Set logger levels using settings.
Args:
verbose (bool, optional): _description_. Defaults to False.
verbosit (int, optional): Level of verbosity desired 3 is highest. Defaults to 3.
Returns:
logger: logger object

77
src/submissions/frontend/__init__.py
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@@ -3,6 +3,7 @@ Operations for all user interactions.
'''
import json
import re
import sys
from PyQt6.QtWidgets import (
QMainWindow, QLabel, QToolBar,
QTabWidget, QWidget, QVBoxLayout,
@@ -32,7 +33,7 @@ from backend.db import (construct_submission_info, lookup_reagent,
)
from backend.db import lookup_kittype_by_name
from .functions import extract_form_info
from tools import check_not_nan, check_kit_integrity
from tools import check_not_nan, check_kit_integrity, check_if_app
# from backend.excel.reports import
from frontend.custom_widgets import SubmissionsSheet, AlertPop, QuestionAsker, AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker, ImportReagent
import logging
@@ -40,6 +41,7 @@ import difflib
from getpass import getuser
from datetime import date
from frontend.visualizations import create_charts
import webbrowser
logger = logging.getLogger(f'submissions.{__name__}')
logger.info("Hello, I am a logger")
@@ -49,6 +51,7 @@ class App(QMainWindow):
def __init__(self, ctx: dict = {}):
super().__init__()
self.ctx = ctx
# indicate version and database connected in title bar
try:
self.title = f"Submissions App (v{ctx['package'].__version__}) - {ctx['database']}"
except AttributeError:
@@ -84,6 +87,7 @@ class App(QMainWindow):
maintenanceMenu = menuBar.addMenu("&Monthly")
helpMenu = menuBar.addMenu("&Help")
helpMenu.addAction(self.helpAction)
helpMenu.addAction(self.docsAction)
fileMenu.addAction(self.importAction)
reportMenu.addAction(self.generateReportAction)
maintenanceMenu.addAction(self.joinControlsAction)
@@ -111,6 +115,7 @@ class App(QMainWindow):
self.joinControlsAction = QAction("Link Controls")
self.joinExtractionAction = QAction("Link Ext Logs")
self.helpAction = QAction("&About", self)
self.docsAction = QAction("&Docs", self)
def _connectActions(self):
@@ -129,12 +134,20 @@ class App(QMainWindow):
self.joinControlsAction.triggered.connect(self.linkControls)
self.joinExtractionAction.triggered.connect(self.linkExtractions)
self.helpAction.triggered.connect(self.showAbout)
self.docsAction.triggered.connect(self.openDocs)
def showAbout(self):
output = f"Version: {self.ctx['package'].__version__}\n\nAuthor: {self.ctx['package'].__author__['name']} - {self.ctx['package'].__author__['email']}\n\nCopyright: {self.ctx['package'].__copyright__}"
about = AlertPop(message=output, status="information")
about.exec()
def openDocs(self):
if check_if_app():
url = Path(sys._MEIPASS).joinpath("files", "docs", "index.html")
else:
url = Path("docs\\build\\index.html").absolute()
logger.debug(f"Attempting to open {url}")
webbrowser.get('windows-default').open(f"file://{url.__str__()}")
def importSubmission(self):
@@ -365,24 +378,19 @@ class App(QMainWindow):
# Custom two date picker for start & end dates
dlg = ReportDatePicker()
if dlg.exec():
# labels, values = extract_form_info(dlg)
# info = {item[0]:item[1] for item in zip(labels, values)}
info = extract_form_info(dlg)
logger.debug(f"Report info: {info}")
# find submissions based on date range
subs = lookup_submissions_by_date_range(ctx=self.ctx, start_date=info['start_date'], end_date=info['end_date'])
# convert each object to dict
records = [item.report_dict() for item in subs]
# make dataframe from record dictionaries
df = make_report_xlsx(records=records)
html = make_report_html(df=df, start_date=info['start_date'], end_date=info['end_date'])
# make dataframe from record dictionaries
# df = make_report_xlsx(records=records)
# setup filedialog to handle save location of report
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf").resolve().__str__()
# fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".xlsx")[0])
fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
# logger.debug(f"report output name: {fname}")
# df.to_excel(fname, engine='openpyxl')
with open(fname, "w+b") as f:
pisa.CreatePDF(html, dest=f)
writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
@@ -398,14 +406,7 @@ class App(QMainWindow):
worksheet.column_dimensions[get_column_letter(idx)].width = max_len
except ValueError:
pass
# set_column(idx, idx, max_len) # set column width
# colu = worksheet.column_dimensions["C"]
# style = NamedStyle(name="custom_currency", number_format='Currency')
for cell in worksheet['D']:
# try:
# check = int(cell.row)
# except TypeError:
# continue
if cell.row > 1:
cell.style = 'Currency'
writer.close()
@@ -431,19 +432,11 @@ class App(QMainWindow):
return
# send to kit creator function
result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
# msg = QMessageBox()
# msg.setIcon(QMessageBox.critical)
match result['code']:
case 0:
msg = AlertPop(message=result['message'], status='info')
# msg.setText("Kit added")
# msg.setInformativeText(result['message'])
# msg.setWindowTitle("Kit added")
case 1:
msg = AlertPop(message=result['message'], status='critical')
# msg.setText("Permission Error")
# msg.setInformativeText(result['message'])
# msg.setWindowTitle("Permission Error")
msg.exec()
@@ -467,19 +460,11 @@ class App(QMainWindow):
return
# send to kit creator function
result = create_org_from_yaml(ctx=self.ctx, org=org)
# msg = QMessageBox()
# msg.setIcon(QMessageBox.critical)
match result['code']:
case 0:
msg = AlertPop(message=result['message'], status='information')
# msg.setText("Organization added")
# msg.setInformativeText(result['message'])
# msg.setWindowTitle("Kit added")
case 1:
msg = AlertPop(message=result['message'], status='critical')
# msg.setText("Permission Error")
# msg.setInformativeText(result['message'])
# msg.setWindowTitle("Permission Error")
msg.exec()
@@ -537,20 +522,12 @@ class App(QMainWindow):
controls = get_all_controls_by_type(ctx=self.ctx, con_type=self.con_type, start_date=self.start_date, end_date=self.end_date)
# if no data found from query set fig to none for reporting in webview
if controls == None:
# return
fig = None
else:
# data = []
# for control in controls:
# # change each control to list of dicts
# # dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=self.mode)
# dicts = control.convert_by_mode(mode=self.mode)
# data.append(dicts)
# change each control to list of dicts
data = [control.convert_by_mode(mode=self.mode) for control in controls]
# flatten data to one dimensional list
data = [item for sublist in data for item in sublist]
# logger.debug(data)
# send to dataframe creator
df = convert_data_list_to_df(ctx=self.ctx, input=data, subtype=self.subtype)
if self.subtype == None:
@@ -567,16 +544,12 @@ class App(QMainWindow):
else:
html += "<h1>No data was retrieved for the given parameters.</h1>"
html += '</body></html>'
# with open("C:\\Users\\lwark\\Desktop\\test.html", "w") as f:
# f.write(html)
# add html to webview and update.
self.table_widget.webengineview.setHtml(html)
self.table_widget.webengineview.update()
logger.debug("Figure updated... I hope.")
def linkControls(self):
# all_bcs = self.ctx['database_session'].query(models.BacterialCulture).all()
all_bcs = lookup_all_submissions_by_type(self.ctx, "Bacterial Culture")
logger.debug(all_bcs)
all_controls = get_all_controls(self.ctx)
@@ -588,9 +561,6 @@ class App(QMainWindow):
samples = [sample.sample_id for sample in bcs.samples]
logger.debug(bcs.controls)
for sample in samples:
# if "Jan" in sample and "EN" in sample:
# sample = sample.replace("EN-", "EN1-")
# logger.debug(f"Checking for {sample}")
# replace below is a stopgap method because some dingus decided to add spaces in some of the ATCC49... so it looks like "ATCC 49"...
if " " in sample:
logger.warning(f"There is not supposed to be a space in the sample name!!!")
@@ -601,10 +571,8 @@ class App(QMainWindow):
else:
for control in all_controls:
diff = difflib.SequenceMatcher(a=sample, b=control.name).ratio()
# if diff > 0.955:
if control.name.startswith(sample):
logger.debug(f"Checking {sample} against {control.name}... {diff}")
# if sample == control.name:
logger.debug(f"Found match:\n\tSample: {sample}\n\tControl: {control.name}\n\tDifference: {diff}")
if control in bcs.controls:
logger.debug(f"{control.name} already in {bcs.rsl_plate_num}, skipping")
@@ -618,28 +586,22 @@ class App(QMainWindow):
self.ctx["database_session"].add(control)
count += 1
self.ctx["database_session"].add(bcs)
# logger.debug(f"To be added: {ctx['database_session'].new}")
logger.debug(f"Here is the new control: {[control.name for control in bcs.controls]}")
# p = ctx["database_session"].query(models.BacterialCulture).filter(models.BacterialCulture.rsl_plate_num==bcs.rsl_plate_num).first()
result = f"We added {count} controls to bacterial cultures."
logger.debug(result)
# logger.debug(ctx["database_session"].new)
self.ctx['database_session'].commit()
msg = QMessageBox()
# msg.setIcon(QMessageBox.critical)
msg.setText("Controls added")
msg.setInformativeText(result)
msg.setWindowTitle("Controls added")
msg.exec()
def linkExtractions(self):
home_dir = str(Path(self.ctx["directory_path"]))
fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "csv(*.csv)")[0])
with open(fname.__str__(), 'r') as f:
runs = [col.strip().split(",") for col in f.readlines()]
# check = []
count = 0
for run in runs:
obj = dict(
@@ -652,21 +614,14 @@ class App(QMainWindow):
)
for ii in range(6, len(run)):
obj[f"column{str(ii-5)}_vol"] = run[ii]
# check.append(json.dumps(obj))
# sub = self.ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num.startswith(obj["rsl_plate_num"])).first()
sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=obj['rsl_plate_num'])
try:
logger.debug(f"Found submission: {sub.rsl_plate_num}")
count += 1
except AttributeError:
continue
# output = json.dumps(obj)
if sub.extraction_info != None:
# try:
# logger.debug(f"Attempting update on ext info: {sub.extraction_info} for {sub.rsl_plate_num}")
existing = json.loads(sub.extraction_info)
# except:
# existing = None
else:
existing = None
try:
@@ -677,7 +632,6 @@ class App(QMainWindow):
pass
if existing != None:
try:
# sub.extraction_info += output
logger.debug(f"Updating {type(existing)}: {existing} with {type(obj)}: {obj}")
existing.append(obj)
logger.debug(f"Setting: {existing}")
@@ -694,7 +648,6 @@ class App(QMainWindow):
dlg.exec()
class AddSubForm(QWidget):
def __init__(self, parent):

5
src/submissions/frontend/custom_widgets/misc.py
View File

@@ -294,7 +294,10 @@ class ImportReagent(QComboBox):
self.setEditable(True)
# Ensure that all reagenttypes have a name that matches the items in the excel parser
query_var = item.replace("lot_", "")
logger.debug(f"Import Reagent is looking at: {prsr.sub[item]} for {item}")
if prsr != None:
logger.debug(f"Import Reagent is looking at: {prsr.sub[item]} for {item}")
else:
logger.debug(f"Import Reagent is going to retrieve all reagents for {item}")
logger.debug(f"Query for: {query_var}")
if prsr != None:
if isinstance(prsr.sub[item], np.float64):

11
src/submissions/frontend/custom_widgets/sub_details.py
View File

@@ -50,7 +50,7 @@ class pandasModel(QAbstractTableModel):
does what it says
Args:
parnet (_type_, optional): _description_. Defaults to None.
parent (_type_, optional): _description_. Defaults to None.
Returns:
int: number of columns in data
@@ -140,6 +140,12 @@ class SubmissionsSheet(QTableView):
def delete_item(self, event):
"""
Confirms user deletion and sends id to backend for deletion.
Args:
event (_type_): _description_
"""
index = (self.selectionModel().currentIndex())
value = index.sibling(index.row(),0).data()
logger.debug(index)
@@ -201,6 +207,9 @@ class SubmissionDetails(QDialog):
def export(self):
"""
Renders submission to html, then creates and saves .pdf file to user selected file.
"""
template = env.get_template("submission_details.html")
html = template.render(sub=self.base_dict)
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()

7
src/submissions/frontend/functions.py
View File

@@ -1,3 +1,6 @@
'''
contains operations used by multiple widgets.
'''
from backend.db.models import *
import logging
from PyQt6.QtWidgets import (
@@ -43,9 +46,7 @@ def extract_form_info(object) -> dict:
dicto[item.objectName()] = item.value()
case ReagentTypeForm():
reagent = extract_form_info(item)
# reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
logger.debug(reagent)
# reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
logger.debug(f"Reagent found: {reagent}")
reagents[reagent["name"].strip()] = {'eol_ext':int(reagent['eol'])}
# value for ad hoc check above
if reagents != {}:

51
src/submissions/tools/__init__.py
View File

@@ -1,3 +1,7 @@
'''
Contains miscellaenous functions used by both frontend and backend.
'''
import sys
import numpy as np
import logging
import getpass
@@ -6,6 +10,15 @@ from backend.db.models import BasicSubmission, KitType
logger = logging.getLogger(f"submissions.{__name__}")
def check_not_nan(cell_contents) -> bool:
"""
Check to ensure excel sheet cell contents are not blank.
Args:
cell_contents (_type_): The contents of the cell in question.
Returns:
bool: True if cell has value, else, false.
"""
# check for nan as a string first
if cell_contents == 'nan':
cell_contents = np.nan
@@ -19,6 +32,15 @@ def check_not_nan(cell_contents) -> bool:
def check_is_power_user(ctx:dict) -> bool:
"""
Check to ensure current user is in power users list.
Args:
ctx (dict): settings passed down from gui.
Returns:
bool: True if user is in power users, else false.
"""
try:
check = getpass.getuser() in ctx['power_users']
except KeyError as e:
@@ -30,6 +52,15 @@ def check_is_power_user(ctx:dict) -> bool:
def create_reagent_list(in_dict:dict) -> list[str]:
"""
Makes list of reagent types without "lot\_" prefix for each key in a dictionary
Args:
in_dict (dict): input dictionary of reagents
Returns:
list[str]: list of reagent types with "lot\_" prefix removed.
"""
return [item.strip("lot_") for item in in_dict.keys()]
@@ -67,5 +98,21 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
result = None
else:
# missing = [x for x in ext_kit_rtypes if x not in common]
result = {'message' : f"Couldn't verify reagents match listed kit components.\n\nIt looks like you are missing: {[item.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.", 'missing': missing}
return result
result = {'message' : f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", 'missing': missing}
return result
def check_if_app(ctx:dict=None) -> bool:
"""
Checks if the program is running from pyinstaller compiled
Args:
ctx (dict, optional): Settings passed down from gui. Defaults to None.
Returns:
bool: True if running from pyinstaller. Else False.
"""
if getattr(sys, 'frozen', False):
return True
else:
return False